Drosophila melanogaster vs Culex quinquefasciatus LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Culex quinquefasciatus (Culex quinquefasciatus, CpipJ2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 78. Drosophila melanogaster was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 46,258

Genome coverage (bp) Coding exon coverage (bp)
Drosophila melanogaster

Uncovered: 131,436,688 out of 143,725,995
Covered: 12,289,307 out of 143,725,995

Uncovered: 11,725,609 out of 22,883,909
Matches: 7,312,043 out of 22,883,909
Mismatches: 3,471,053 out of 22,883,909
Insertions: 375,204 out of 22,883,909

Culex quinquefasciatus

Uncovered: 565,086,291 out of 579,057,705
Covered: 13,971,414 out of 579,057,705

Uncovered: 13,290,189 out of 24,940,576
Matches: 7,674,437 out of 24,940,576
Mismatches: 3,643,469 out of 24,940,576
Insertions: 332,481 out of 24,940,576

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Drosophila melanogaster Culex quinquefasciatus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}